part of
type: ObjectProperty
equivalent property:
  inverse of: has part
inverse of: has part
type: TransitiveProperty
IAO_0000111: is part of
IAO_0000112: my brain is part of my body (continuant parthood, two material entities)
IAO_0000112: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
IAO_0000112: this day is part of this year (occurrent parthood)
IAO_0000115: a core relation that holds between a part and its whole
IAO_0000116: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
IAO_0000118: part_of
IAO_0000412: obi.owl
RO_0001900: RO_0001901

has part
type: ObjectProperty
type: TransitiveProperty
IAO_0000111: has part
IAO_0000112: my body has part my brain (continuant parthood, two material entities)
IAO_0000112: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
IAO_0000112: this year has part this day (occurrent parthood)
IAO_0000115: a core relation that holds between a whole and its part
IAO_0000116: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
IAO_0000118: has_part
IAO_0000412: obi.owl
RO_0001900: RO_0001901

realized in
type: ObjectProperty
equivalent property:
  inverse of: realizes
inverse of: realizes
IAO_0000111: realized in
IAO_0000112: this disease is realized in this disease course
IAO_0000112: this fragility is realized in this shattering
IAO_0000112: this investigator role is realized in this investigation
IAO_0000118: is realized by
IAO_0000118: realized_in
IAO_0000412: obi.owl
IAO_0000600: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
IAO_0000111: realizes
IAO_0000112: this disease course realizes this disease
IAO_0000112: this investigation realizes this investigator role
IAO_0000112: this shattering realizes this fragility
IAO_0000412: obi.owl
IAO_0000600: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

preceded by
type: ObjectProperty
inverse of: precedes
type: TransitiveProperty
IAO_0000111: preceded by
IAO_0000116: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
IAO_0000118: is preceded by
IAO_0000118: preceded_by
IAO_0000412: obi.owl
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by

precedes
type: ObjectProperty
sub property of: temporal relation
type: TransitiveProperty
IAO_0000111: precedes
IAO_0000412: obi.owl

has measurement unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
IAO_0000412: obi.owl

is about
type: ObjectProperty
domain: information content entity
IAO_0000112: This document is about information artifacts and their representations
IAO_0000114: pending final vetting
IAO_0000115: is_about is a (currently) primitive relation that relates an information artifact to an entity.
IAO_0000116: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
IAO_0000117: person:Alan Ruttenberg
IAO_0000119: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
IAO_0000412: obi.owl

denotes
type: ObjectProperty
sub property of: is about
inverse of: is denoted by
IAO_0000112: A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
IAO_0000115: denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
IAO_0000116: 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
IAO_0000117: person:Alan Ruttenberg
IAO_0000119: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
IAO_0000412: obi.owl

is_supported_by_data
type: ObjectProperty
IAO_0000111: is_supported_by_data
IAO_0000112: The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
IAO_0000114: ready for release
IAO_0000115: The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
IAO_0000117: OBI
IAO_0000119: OBI
IAO_0000119: Philly 2011 workshop
IAO_0000412: obi.owl

has_specified_input
type: ObjectProperty
equivalent property:
  inverse of: is_specified_input_of
sub property of: has participant
inverse of: is_specified_input_of
IAO_0000111: has_specified_input
IAO_0000112: see is_input_of example_of_usage
IAO_0000114: ready for release
IAO_0000115: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
IAO_0000116: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Larry Hunter
IAO_0000117: PERSON: Melanie Coutot
IAO_0000412: obi.owl

is_specified_input_of
type: ObjectProperty
sub property of: participates in
IAO_0000111: is_specified_input_of
IAO_0000112: some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
IAO_0000114: ready for release
IAO_0000115: A relation between a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
IAO_0000117: Alan Ruttenberg
IAO_0000117: PERSON:Bjoern Peters
IAO_0000412: obi.owl

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has participant
inverse of: is_specified_output_of
IAO_0000111: has_specified_output
IAO_0000114: ready for release
IAO_0000115: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Larry Hunter
IAO_0000117: PERSON: Melanie Courtot
IAO_0000412: obi.owl

is_specified_output_of
type: ObjectProperty
sub property of: participates in
IAO_0000111: is_specified_output_of
IAO_0000114: ready for release
IAO_0000115: A relation between a continuant participating in a planned process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
IAO_0000117: Alan Ruttenberg
IAO_0000117: PERSON:Bjoern Peters
IAO_0000412: obi.owl

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
IAO_0000111: achieves_planned_objective
IAO_0000112: A cell sorting process achieves the objective specification 'material separation objective'
IAO_0000114: metadata complete
IAO_0000115: This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
IAO_0000117: BP, AR, PPPB branch
IAO_0000119: PPPB branch derived
IAO_0000232: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
IAO_0000412: obi.owl

objective_achieved_by
type: ObjectProperty
IAO_0000111: objective_achieved_by
IAO_0000114: ready for release
IAO_0000115: This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
IAO_0000117: OBI
IAO_0000119: OBI
IAO_0000412: obi.owl

has value specification
type: ObjectProperty
sub property of: has part
domain: information content entity
range: value specification
IAO_0000111: has value specification
IAO_0000114: metadata complete
IAO_0000115: A relation between an information content entity and a value specification that specifies its value.
IAO_0000117: PERSON: James A. Overton
IAO_0000119: OBI
IAO_0000412: obi.owl

inheres in
type: ObjectProperty
equivalent property:
  inverse of: bearer of
inverse of: bearer of
IAO_0000111: inheres in
IAO_0000112: this fragility inheres in this vase
IAO_0000112: this red color inheres in this apple
IAO_0000115: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
IAO_0000116: A dependent inheres in its bearer at all times for which the dependent exists.
IAO_0000118: inheres_in
IAO_0000412: obi.owl
RO_0001900: RO_0001901

bearer of
type: ObjectProperty
IAO_0000111: bearer of
IAO_0000112: this apple is bearer of this red color
IAO_0000112: this vase is bearer of this fragility
IAO_0000115: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
IAO_0000118: bearer_of
IAO_0000118: is bearer of
IAO_0000412: obi.owl
RO_0001900: RO_0001901

participates in
type: ObjectProperty
equivalent property:
  inverse of: has participant
inverse of: has participant
IAO_0000111: participates in
IAO_0000112: this blood clot participates in this blood coagulation
IAO_0000112: this input material (or this output material) participates in this process
IAO_0000112: this investigator participates in this investigation
IAO_0000115: a relation between a continuant and a process, in which the continuant is somehow involved in the process
IAO_0000118: participates_in
IAO_0000412: obi.owl

has participant
type: ObjectProperty
property chain axiom: has part
IAO_0000111: has participant
IAO_0000112: this blood coagulation has participant this blood clot
IAO_0000112: this investigation has participant this investigator
IAO_0000112: this process has participant this input material (or this output material)
IAO_0000115: a relation between a process and a continuant, in which the continuant is somehow involved in the process
IAO_0000116: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
IAO_0000118: has_participant
IAO_0000412: obi.owl
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
equivalent property:
  inverse of: concretizes
inverse of: concretizes
IAO_0000112: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
IAO_0000112: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
IAO_0000115: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
IAO_0000412: obi.owl

concretizes
type: ObjectProperty
IAO_0000112: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
IAO_0000112: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
IAO_0000115: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
IAO_0000412: obi.owl

quality of
type: ObjectProperty
equivalent property:
  inverse of: has quality
sub property of: inheres in
inverse of: has quality
IAO_0000112: this red color is a quality of this apple
IAO_0000115: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
IAO_0000116: A quality inheres in its bearer at all times for which the quality exists.
IAO_0000118: is quality of
IAO_0000118: quality_of
IAO_0000412: obi.owl

role of
type: ObjectProperty
equivalent property:
  inverse of: has role
sub property of: inheres in
inverse of: has role
IAO_0000112: this investigator role is a role of this person
IAO_0000115: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
IAO_0000116: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
IAO_0000118: is role of
IAO_0000118: role_of
IAO_0000412: obi.owl

has quality
type: ObjectProperty
sub property of: bearer of
IAO_0000112: this apple has quality this red color
IAO_0000115: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
IAO_0000118: has_quality
IAO_0000412: obi.owl

has role
type: ObjectProperty
sub property of: bearer of
IAO_0000112: this person has role this investigator role (more colloquially: this person has this role of investigator)
IAO_0000115: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
IAO_0000118: has_role
IAO_0000412: obi.owl

temporal relation
type: ObjectProperty
IAO_0000114: pending final vetting
IAO_0000116: move to BFO?
IAO_0000119: Allen
IAO_0000412: obi.owl
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

declares
type: ObjectProperty
sub property of: is about
inverse of: is declared by
IAO_0000115: property to indicate that a design declares a variable; the inverse property is 'is declared by'
IAO_0000117: Alejandra Gonzalez-Beltran
IAO_0000117: Orlaith Burke
IAO_0000117: Philippe Rocca-Serra

is declared by
type: ObjectProperty
IAO_0000115: property to indicate the variables declared by a design; the inverse property is 'declares'
IAO_0000117: Alejandra Gonzalez-Beltran
IAO_0000117: Orlaith Burke
IAO_0000117: Philippe Rocca-Serra

has numerator
type: ObjectProperty
type: AsymmetricProperty
IAO_0000115: the relationship between a fraction and the number above the line
IAO_0000117: Alejandra Gonzalez-Beltran
IAO_0000117: Orlaith Burke
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: AGB

is member of
type: ObjectProperty
inverse of: has member
IAO_0000115: relationship between an element and a set it belongs to
IAO_0000117: Alejandra Gonzalez-Beltran
IAO_0000117: Orlaith Burke
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: AGB

has member
type: ObjectProperty
IAO_0000115: relationship between a set and one of its elements
IAO_0000117: Alejandra Gonzalez-Beltran
IAO_0000117: Orlaith Burke
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: AGB

is denoted by
type: ObjectProperty
IAO_0000115: Inverse relation of 'denotes', where denotation is what happens when someone creates an information content entity E in order to specifically refer to something (from 'denotes' definition).
IAO_0000117: Alejandra Gonzalez-Beltran
IAO_0000117: Orlaith Burke
IAO_0000117: Philippe Rocca-Serra

has denominator
type: ObjectProperty
IAO_0000115: the relationship between a fraction and the number below the line (or divisor)
IAO_0000117: Alejandra Gonzalez-Beltran
IAO_0000117: Orlaith Burke
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: AGB

is model for
type: ObjectProperty
inverse of: is modeled by
IAO_0000115: This property is the inverse relationship of 'is model by' and represents the relationship between a dependent variable and an statistical model.
IAO_0000117: Alejandra Gonzalez-Beltran
IAO_0000117: Philippe Rocca-Serra

has effect on
type: ObjectProperty
sub property of: is about
IAO_0000114: requires discussion
IAO_0000115: 'has effect on' is a special case of the 'is about' relationship to be used for mixed effect models
IAO_0000116: AGB: this relationship requires more discussion in light of potentially adding the Effect class as per the issue: https://github.com/ISA-tools/stato/issues/75 Thus the definition is temporary. The domain and range were 'variable' but removing now to discuss the specific restrictions when the issue is discussed. Not extracting to separate ontology (stato-experimental.owl) due to IDs already assigned. If deemed not necessary in the future, the IDs should be deprecated.
IAO_0000117: Alejandra Gonzalez-Beltran
IAO_0000117: Philippe Rocca-Serra

estimate of
type: ObjectProperty
IAO_0000115: Relationship between a parameter of a model and the estimate produced by estimation process as used in statistical modeling.

is modeled by
type: ObjectProperty
sub property of: is about
IAO_0000115: This property is a specialization of the 'is about' property to represent the relationship between a dependent variable and an statistical model.
IAO_0000117: Alejandra Gonzalez-Beltran
IAO_0000117: Philippe Rocca-Serra

has measurement value
type: DatatypeProperty
type: FunctionalProperty
domain: scalar measurement datum
range: double
IAO_0000412: obi.owl

has specified numeric value
type: DatatypeProperty
sub property of: has specified value
domain: value specification
range: real
IAO_0000111: has specified numeric value
IAO_0000114: metadata complete
IAO_0000115: A relation between a value specification and a number that quantifies it.
IAO_0000116: A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
IAO_0000117: PERSON: James A. Overton
IAO_0000119: OBI
IAO_0000412: obi.owl

has specified value
type: DatatypeProperty
domain: value specification
IAO_0000111: has specified value
IAO_0000114: metadata incomplete
IAO_0000115: A relation between a value specification and a literal.
IAO_0000116: This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
IAO_0000119: OBI
IAO_0000412: obi.owl

has value
type: DatatypeProperty
IAO_0000115: A relationship (data property) between an entity and its value.
IAO_0000117: Alejandra Gonzalez-Beltran
IAO_0000117: Orlaith Burke
IAO_0000117: Philippe Rocca-Serra

material entity
type: Class
BFO_0000179: material
BFO_0000180: MaterialEntity
IAO_0000112: a flame
IAO_0000112: a forest fire
IAO_0000112: a human being
IAO_0000112: a hurricane
IAO_0000112: a photon
IAO_0000112: a puff of smoke
IAO_0000112: a sea wave
IAO_0000112: a tornado
IAO_0000112: an aggregate of human beings.
IAO_0000112: an energy wave
IAO_0000112: an epidemic
IAO_0000112: the undetached arm of a human being
IAO_0000115: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
IAO_0000116: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
IAO_0000116: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
IAO_0000116: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
IAO_0000412: obi.owl
IAO_0000600: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
IAO_0000601: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
IAO_0000601: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
IAO_0000602: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
IAO_0000602: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
IAO_0000602: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]

information content entity
type: Class
IAO_0000111: information content entity
IAO_0000112: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
IAO_0000114: ready for release
IAO_0000115: A generically dependent continuant that is about some thing.
IAO_0000116: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
IAO_0000116: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000119: OBI_0000142
IAO_0000412: obi.owl

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: scalar value specification
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
IAO_0000112: 10 feet. 3 ml.
IAO_0000114: metadata complete
IAO_0000115: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
IAO_0000116: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
IAO_0000116: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Melanie Courtot
IAO_0000412: obi.owl

measurement datum
type: Class
subclass of: Restriction
  on property: has value specification
  some values from: value specification
IAO_0000111: measurement datum
IAO_0000112: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
IAO_0000114: pending final vetting
IAO_0000115: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
IAO_0000116: 2/2/2009 is_specified_output of some assay?
IAO_0000117: person:Chris Stoeckert
IAO_0000119: OBI_0000305
IAO_0000119: group:OBI
IAO_0000412: obi.owl

material sample role
type: Class
IAO_0000111: material sample role
IAO_0000112: a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
IAO_0000114: pending final vetting
IAO_0000115: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
IAO_0000116: 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
IAO_0000412: obi.owl

material sample
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: specimen
IAO_0000111: material sample
IAO_0000112: blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
IAO_0000114: metadata incomplete
IAO_0000115: A material entity that has the material sample role
IAO_0000117: OBI: workshop
IAO_0000118: sample population
IAO_0000412: obi.owl
OBI_0001847: sample

scalar value specification
type: Class
subclass of: value specification
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has specified numeric value
  min cardinality: 1
IAO_0000111: scalar value specification
IAO_0000114: metadata incomplete
IAO_0000115: A value specification that consists of two parts: a numeral and a unit label
IAO_0000117: PERSON:Bjoern Peters
IAO_0000412: obi.owl

value specification
type: Class
subclass of: information content entity
IAO_0000111: value specification
IAO_0000112: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
IAO_0000114: ready for release
IAO_0000115: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
IAO_0000116: This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
IAO_0000117: PERSON:Bjoern Peters
IAO_0000412: obi.owl

specimen
type: Class
subclass of: material entity
IAO_0000111: specimen
IAO_0000112: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
IAO_0000114: ready for release
IAO_0000115: A material entity that has the specimen role.
IAO_0000116: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
IAO_0000117: PERSON: James Malone
IAO_0000117: PERSON: Philippe Rocca-Serra
IAO_0000119: GROUP: OBI Biomaterial Branch
IAO_0000412: obi.owl

example to be eventually removed

metadata complete
IAO_0000115: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

organizational term
IAO_0000115: term created to ease viewing/sort terms for development purpose, and will not be included in a release
IAO_0000117: PERSON:Alan Ruttenberg

ready for release
IAO_0000115: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

metadata incomplete
IAO_0000115: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
IAO_0000115: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
IAO_0000115: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.

to be replaced with external ontology term
IAO_0000115: Terms with this status should eventually replaced with a term from another ontology.
IAO_0000117: Alan Ruttenberg
IAO_0000119: group:OBI

requires discussion
IAO_0000115: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
IAO_0000117: Alan Ruttenberg
IAO_0000119: group:OBI